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Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.

Aquaculture Genomics, Genetics and Breeding Workshop., Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Kahlil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KF, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T.

BMC Genomics. 2017 Feb 20;18(1):191. doi: 10.1186/s12864-017-3557-1. Erratum in: BMC Genomics. 2017 Mar 16;18(1):235.


OMWare: a tool for efficient assembly of genome-wide physical maps.

Sharp AR, Udall JA.

BMC Bioinformatics. 2016 Jul 25;17 Suppl 7:241. doi: 10.1186/s12859-016-1099-1.


Allele-Specific Quantification of Structural Variations in Cancer Genomes.

Li Y, Zhou S, Schwartz DC, Ma J.

Cell Syst. 2016 Jul;3(1):21-34. doi: 10.1016/j.cels.2016.05.007. Epub 2016 Jul 21.


Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits.

Eckshtain-Levi N, Shkedy D, Gershovits M, Da Silva GM, Tamir-Ariel D, Walcott R, Pupko T, Burdman S.

Front Microbiol. 2016 Apr 6;7:430. doi: 10.3389/fmicb.2016.00430. eCollection 2016 Apr 6.


Bacterial genomic epidemiology, from local outbreak characterization to species-history reconstruction.

Gaiarsa S, De Marco L, Comandatore F, Marone P, Bandi C, Sassera D.

Pathog Glob Health. 2015;109(7):319-27. doi: 10.1080/20477724.2015.1103503. Review.


Analysis of single nucleic acid molecules in micro- and nano-fluidics.

Friedrich SM, Zec HC, Wang TH.

Lab Chip. 2016 Mar 7;16(5):790-811. doi: 10.1039/c5lc01294e. Review.


Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates.

Yuan B, Liu P, Gupta A, Beck CR, Tejomurtula A, Campbell IM, Gambin T, Simmons AD, Withers MA, Harris RA, Rogers J, Schwartz DC, Lupski JR.

PLoS Genet. 2015 Dec 7;11(12):e1005686. doi: 10.1371/journal.pgen.1005686. eCollection 2015 Dec 7.


Image processing for optical mapping.

Ravindran P, Gupta A.

Gigascience. 2015 Nov 26;4:57. doi: 10.1186/s13742-015-0096-z. eCollection 2015 Nov 26. Review.


De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.

Olsen RA, Bunikis I, Tiukova I, Holmberg K, Lötstedt B, Pettersson OV, Passoth V, Käller M, Vezzi F.

Gigascience. 2015 Nov 26;4:56. doi: 10.1186/s13742-015-0094-1. eCollection 2015 Nov 26.


Molecular tools in understanding the evolution of Vibrio cholerae.

Rahaman MH, Islam T, Colwell RR, Alam M.

Front Microbiol. 2015 Oct 6;6:1040. doi: 10.3389/fmicb.2015.01040. eCollection 2015 Oct 6. Review.


Genetic variation and the de novo assembly of human genomes.

Chaisson MJ, Wilson RK, Eichler EE.

Nat Rev Genet. 2015 Nov;16(11):627-40. doi: 10.1038/nrg3933. Epub 2015 Oct 7. Review.


Visualizing the entire DNA from a chromosome in a single frame.

Freitag C, Noble C, Fritzsche J, Persson F, Reiter-Schad M, Nilsson AN, Granéli A, Ambjörnsson T, Mir KU, Tegenfeldt JO.

Biomicrofluidics. 2015 Aug 5;9(4):044114. doi: 10.1063/1.4923262. eCollection 2015 Aug 5.


Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools.

Fierst JL.

Front Genet. 2015 Jun 19;6:220. doi: 10.3389/fgene.2015.00220. eCollection 2015 Jun 19. Review.


Best Practices in Insect Genome Sequencing: What Works and What Doesn't.

Richards S, Murali SC.

Curr Opin Insect Sci. 2015 Feb 1;7:1-7.


Misassembly detection using paired-end sequence reads and optical mapping data.

Muggli MD, Puglisi SJ, Ronen R, Boucher C.

Bioinformatics. 2015 Jun 15;31(12):i80-8. doi: 10.1093/bioinformatics/btv262.


Clostridium sordellii genome analysis reveals plasmid localized toxin genes encoded within pathogenicity loci.

Couchman EC, Browne HP, Dunn M, Lawley TD, Songer JG, Hall V, Petrovska L, Vidor C, Awad M, Lyras D, Fairweather NF.

BMC Genomics. 2015 May 16;16:392. doi: 10.1186/s12864-015-1613-2.


A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings.

Noble C, Nilsson AN, Freitag C, Beech JP, Tegenfeldt JO, Ambjörnsson T.

PLoS One. 2015 Apr 13;10(4):e0121905. doi: 10.1371/journal.pone.0121905. eCollection 2015 Apr 13.


Using optical mapping data for the improvement of vertebrate genome assemblies.

Howe K, Wood JM.

Gigascience. 2015 Mar 18;4:10. doi: 10.1186/s13742-015-0052-y. eCollection 2015 Mar 18. Review.


Optical mapping in plant comparative genomics.

Tang H, Lyons E, Town CD.

Gigascience. 2015 Feb 10;4:3. doi: 10.1186/s13742-015-0044-y. eCollection 2015 Feb 10. Review.


Computational methods for optical mapping.

Mendelowitz L, Pop M.

Gigascience. 2014 Dec 30;3(1):33. doi: 10.1186/2047-217X-3-33. eCollection 2014 Dec 30. Review.

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